Batch Information

Batch B002
N Samples 24
N Pools 2
B002-P1 Samples IMM19_698, PB00004-01, PB00006-01, PB00010-01, PB00011-01, PB00012-01, PB00013-01, PB00014-01, PB00015-01, PB00016-01, PB00017-01, PB00018-01, PB00019-01
B002-P2 Samples IMM19_698, PB00020-01, PB00021-01, PB00022-01, PB00024-01, PB00053-01, PB00055-01, PB00056-01, PB00057-01, PB00059-01, PB00060-01, PB00061-01, PB00062-01

QC Results Summary

Category Results Description
Well Sequencing and Alignment Warning
Cell Hashing Pass
Cell Labeling Pass
Control Sample Pass

Summary Details

Well Sequencing and Alignment

The following metrics summarize the sequencing and alignment by 10x well prior to un-hashing and hash-based cell filtering.

Detailed Well Summary

Spec Median_Range Inter_Well_CV Comments Plot
estimated_number_of_cells 27038 (21882-33097) 11.2% Fail: message
fraction_reads_in_cells 93.5 (92.1-94.9) 0.9%
mean_reads_per_cell 32890 (26087-43885) 11.7%
median_genes_per_cell 1594 (1500-1796) 3.6% Warning: message
median_umi_counts_per_cell 5309 (4848-6153) 5.0%
number_of_reads 920541389 (791967202-1088565134) 6.9%
q30_bases_in_barcode 95.6 (95.5-96.2) 0.4%
q30_bases_in_rna_read 93.8 (93.2-94.7) 0.5%
q30_bases_in_sample_index 93.7 (90.9-95.2) 1.2%
q30_bases_in_umi 95.4 (95.3-96.1) 0.4%
reads_mapped_antisense_to_gene 1.9 (1.7-2.1) 5.9%
reads_mapped_confidently_to_exonic_regions 64.8 (60.1-66.4) 2.7%
reads_mapped_confidently_to_genome 91.1 (88.3-92.4) 1.2%
reads_mapped_confidently_to_intergenic_regions 3.9 (3.8-4.2) 2.8%
reads_mapped_confidently_to_intronic_regions 22.7 (21.1-24.8) 3.8% Warning: message
reads_mapped_confidently_to_transcriptome 60.2 (55.4-62.1) 3.1%
reads_mapped_to_genome 95.3 (92.9-96.3) 1.0%
sequencing_saturation 64.4 (56.0-68.9) 5.1% Warning: message
total_genes_detected 24169 (23735-24554) 1.1% Warning: message
valid_barcodes 97.2 (97.0-97.4) 0.1%

Cell Hashing

Specification Value Comments
x x
x x
x x Warning: message
x x Fail: mesage
x x

HTO Assignment Cutoffs

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HTO Category Counts by Well

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HTO Category Fraction by Well

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Singlet Summaries (hash-based)

HTO Barcode Count per Well Plot

##### HTO Barcode Fraction per Well Plot

Well Fraction per HTO Barcode Plot

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Counts by HTO Category and Barcode
## Warning: Removed 2 rows containing non-finite values (stat_ydensity).

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## Warning: Removed 3 rows containing non-finite values (stat_ydensity).
## Warning: Removed 2 rows containing non-finite values (stat_ydensity).

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Cell Labeling

Specification Value Comments
x x
x x
x x Warning: message
x x Fail: mesage
x x

UMAP

## Warning: [ONE-TIME WARNING] Forked processing ('multicore') is disabled
## in future (>= 1.13.0) when running R from RStudio, because it is
## considered unstable. Because of this, plan("multicore") will fall
## back to plan("sequential"), and plan("multiprocess") will fall back to
## plan("multisession") - not plan("multicore") as in the past. For more details,
## how to control forked processing or not, and how to silence this warning in
## future R sessions, see ?future::supportsMulticore
## Warning: Non-unique features (rownames) present in the input matrix, making
## unique
## Centering and scaling data matrix
## PC_ 1 
## Positive:  MNDA, FCN1, FGL2, CST3, CYBB, SERPINA1, CTSS, CSTA, NCF2, LYZ 
##     IGSF6, VCAN, S100A9, LST1, AIF1, PSAP, SPI1, TYROBP, CD68, MS4A6A 
##     CD14, TYMP, MPEG1, CPVL, S100A8, AC020656.1, GRN, CD302, CLEC12A, FCER1G 
## Negative:  IL7R, LTB, IL32, TRBC2, TRBC1, ISG20, HIST1H1D, SYNE2, MAL, GZMM 
##     HIST1H4C, RORA, AQP3, CTSW, SAMD3, CD69, CCL5, KLRB1, CD8B, GZMA 
##     ARID5B, PASK, GPR183, PYHIN1, CST7, FKBP11, AC013264.1, TSHZ2, CD8A, KLRG1 
## PC_ 2 
## Positive:  CD79A, MS4A1, IGHM, BANK1, IGHD, TCL1A, RALGPS2, LINC00926, CD79B, HLA-DQA1 
##     TNFRSF13C, VPREB3, FCER2, HLA-DQB1, IGKC, FCRL1, LINC02397, AFF3, HLA-DRA, SPIB 
##     BCL11A, CD22, MEF2C, SWAP70, FAM129C, HLA-DRB1, FCRLA, GNG7, COBLL1, HVCN1 
## Negative:  NKG7, CST7, GZMA, KLRD1, CTSW, PRF1, CCL5, FGFBP2, HOPX, GZMM 
##     GNLY, CCL4, KLRF1, GZMB, TRDC, MATK, SPON2, S100A4, SAMD3, EFHD2 
##     GZMH, KLRB1, CLIC3, IL2RB, IFITM2, ANXA1, SRGN, FCGR3A, PTGDR, XCL2 
## PC_ 3 
## Positive:  IL7R, MAL, TSHZ2, ADTRP, VIM, AQP3, VCAN, S100A8, PASK, LRRN3 
##     S100A12, LTB, S100A9, CSF3R, CD14, AIF1, CD4, LYZ, FCN1, AC013264.1 
##     AC020656.1, SLC40A1, IL17RA, PLBD1, CD36, CYP1B1, RBP7, MNDA, LINC02446, FPR1 
## Negative:  GZMB, NKG7, CST7, KLRD1, GZMA, CLIC3, PRF1, FGFBP2, KLRF1, HOPX 
##     GNLY, CCL4, CXXC5, PLEK, SPON2, CLIC1, CD79A, FCGR3A, MS4A1, CTSW 
##     CD79B, IGHM, CYBA, GZMH, BANK1, TRDC, APOBEC3G, MATK, PLAC8, CCL5 
## PC_ 4 
## Positive:  MS4A1, IGHD, CD79A, LINC00926, JUN, RALGPS2, FCER2, CD79B, FCRL1, TNFRSF13C 
##     VPREB3, MT-CO1, IGHM, LINC02397, CD22, KLRD1, TCL1A, IER2, CYBA, ZFP36L1 
##     ADAM28, NEAT1, GZMA, PLPP5, SWAP70, NKG7, PAX5, CST7, IL4R, PRF1 
## Negative:  CAVIN2, TUBB1, PPBP, GNG11, PRKAR2B, PF4, CLU, GP9, NRGN, PTCRA 
##     ACRBP, HIST1H2AC, TREML1, MTURN, CMTM5, C2orf88, TSC22D1, SPARC, TMEM40, RGS18 
##     F13A1, MMD, MAP3K7CL, MYL9, RAB27B, RUFY1, HIST1H3H, HIST1H2BJ, CD9, CA2 
## PC_ 5 
## Positive:  SERPINF1, PLD4, LILRA4, IL3RA, CLEC4C, ITM2C, GAS6, TPM2, LRRC26, SMPD3 
##     DERL3, SCT, DNASE1L3, PPP1R14B, LAMP5, IRF7, UGCG, SCN9A, MAP1A, MZB1 
##     LINC00996, JCHAIN, CCDC50, VIM, AL096865.1, MYBL2, PACSIN1, AC097375.1, AC119428.2, TNFRSF21 
## Negative:  CAVIN2, PPBP, TUBB1, PF4, GNG11, NRGN, CLU, GP9, PDLIM1, MT-CO1 
##     PRKAR2B, MS4A1, ACRBP, TREML1, IGHD, HIST1H2AC, RAB27B, CMTM5, BANK1, SPARC 
##     LINC00926, F13A1, RGS18, C2orf88, CD79A, GNLY, MAP3K7CL, TMEM40, TSPAN33, MMD

## Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
## To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
## This message will be shown once per session
## 00:12:14 UMAP embedding parameters a = 0.9922 b = 1.112
## 00:12:14 Read 78210 rows and found 4 numeric columns
## 00:12:14 Using Annoy for neighbor search, n_neighbors = 30
## 00:12:14 Building Annoy index with metric = cosine, n_trees = 50
## 0%   10   20   30   40   50   60   70   80   90   100%
## [----|----|----|----|----|----|----|----|----|----|
## **************************************************|
## 00:12:34 Writing NN index file to temp file /tmp/RtmpUK6jXS/file17813677ee29
## 00:12:34 Searching Annoy index using 1 thread, search_k = 3000
## 00:13:26 Annoy recall = 100%
## 00:13:27 Commencing smooth kNN distance calibration using 1 thread
## 00:13:34 Initializing from normalized Laplacian + noise
## 00:14:07 Commencing optimization for 200 epochs, with 2579154 positive edges
## 00:16:01 Optimization finished
## [1] TRUE

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UMAP Cell Visualizations

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Seurat Labeling Scores

## Warning: Removed 26 rows containing missing values (geom_bar).

Marker Visualization

Leukopak Control

Specification Value Comments
x x
x x
x x Warning: message
x x Fail: mesage
x x

Session Information

Files Analyzed:

##  [1] "B002-P1_IMM19-698_labeled.h5"  "B002-P1_PB00004-01_labeled.h5"
##  [3] "B002-P1_PB00006-01_labeled.h5" "B002-P1_PB00010-01_labeled.h5"
##  [5] "B002-P1_PB00011-01_labeled.h5" "B002-P1_PB00012-01_labeled.h5"
##  [7] "B002-P1_PB00013-01_labeled.h5" "B002-P1_PB00014-01_labeled.h5"
##  [9] "B002-P1_PB00015-01_labeled.h5" "B002-P1_PB00016-01_labeled.h5"
## [11] "B002-P1_PB00017-01_labeled.h5" "B002-P1_PB00018-01_labeled.h5"
## [13] "B002-P1_PB00019-01_labeled.h5" "B002-P2_IMM19-698_labeled.h5" 
## [15] "B002-P2_PB00020-01_labeled.h5" "B002-P2_PB00021-01_labeled.h5"
## [17] "B002-P2_PB00022-01_labeled.h5" "B002-P2_PB00024-01_labeled.h5"
## [19] "B002-P2_PB00053-01_labeled.h5" "B002-P2_PB00055-01_labeled.h5"
## [21] "B002-P2_PB00056-01_labeled.h5" "B002-P2_PB00057-01_labeled.h5"
## [23] "B002-P2_PB00059-01_labeled.h5" "B002-P2_PB00060-01_labeled.h5"
## [25] "B002-P2_PB00061-01_labeled.h5" "B002-P2_PB00062-01_labeled.h5"

Session Info:

## R version 3.6.0 (2019-04-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 9 (stretch)
## 
## Matrix products: default
## BLAS:   /usr/lib/libblas/libblas.so.3.7.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.7.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] future.apply_1.6.0 future_1.19.1      inflection_1.3.5   Seurat_3.2.2      
##  [5] tidyr_1.1.2        immutils_0.0.2     plotly_4.9.2.1     gt_0.2.2          
##  [9] cowplot_1.1.0      dplyr_1.0.2        ggplot2_3.3.2      HTOparser_1.0.12  
## [13] H5weaver_1.0.17    rlang_0.4.8        Matrix_1.2-17      data.table_1.13.2 
## [17] rhdf5_2.28.1      
## 
## loaded via a namespace (and not attached):
##   [1] Rtsne_0.15            colorspace_1.4-1      deldir_0.1-29        
##   [4] ellipsis_0.3.1        ggridges_0.5.2        spatstat.data_1.4-3  
##   [7] farver_2.0.3          leiden_0.3.3          listenv_0.8.0        
##  [10] ggrepel_0.8.1         RSpectra_0.16-0       codetools_0.2-16     
##  [13] splines_3.6.0         knitr_1.28            polyclip_1.10-0      
##  [16] jsonlite_1.6.1        ica_1.0-2             cluster_2.0.8        
##  [19] png_0.1-7             uwot_0.1.8            shiny_1.5.0          
##  [22] sctransform_0.3.1     compiler_3.6.0        httr_1.4.1           
##  [25] backports_1.1.4       assertthat_0.2.1      fastmap_1.0.1        
##  [28] lazyeval_0.2.2        later_1.0.0           htmltools_0.5.0      
##  [31] tools_3.6.0           rsvd_1.0.3            igraph_1.2.4.1       
##  [34] gtable_0.3.0          glue_1.4.1            RANN_2.6.1           
##  [37] reshape2_1.4.3        rappdirs_0.3.1        Rcpp_1.0.1           
##  [40] spatstat_1.64-1       vctrs_0.3.4           nlme_3.1-139         
##  [43] crosstalk_1.1.0.1     lmtest_0.9-38         xfun_0.14            
##  [46] stringr_1.4.0         globals_0.13.1        mime_0.9             
##  [49] miniUI_0.1.1.1        lifecycle_0.2.0       irlba_2.3.3          
##  [52] goftest_1.2-2         MASS_7.3-51.3         zoo_1.8-8            
##  [55] scales_1.1.1          promises_1.1.0        spatstat.utils_1.17-0
##  [58] parallel_3.6.0        RColorBrewer_1.1-2    yaml_2.2.1           
##  [61] reticulate_1.16       pbapply_1.4-3         gridExtra_2.3        
##  [64] sass_0.2.0            rpart_4.1-15          stringi_1.4.3        
##  [67] checkmate_2.0.0       commonmark_1.7        pkgconfig_2.0.2      
##  [70] matrixStats_0.54.0    evaluate_0.14         lattice_0.20-38      
##  [73] ROCR_1.0-11           purrr_0.3.4           tensor_1.5           
##  [76] Rhdf5lib_1.6.3        labeling_0.3          patchwork_1.0.1      
##  [79] htmlwidgets_1.5.1     tidyselect_1.1.0      RcppAnnoy_0.0.16     
##  [82] plyr_1.8.4            magrittr_1.5          R6_2.4.0             
##  [85] generics_0.0.2        pillar_1.4.6          withr_2.1.2          
##  [88] mgcv_1.8-28           fitdistrplus_1.1-1    survival_2.44-1.1    
##  [91] abind_1.4-5           tibble_3.0.4          crayon_1.3.4         
##  [94] KernSmooth_2.23-15    rmarkdown_2.4         grid_3.6.0           
##  [97] digest_0.6.25         xtable_1.8-4          httpuv_1.5.4         
## [100] munsell_0.5.0         viridisLite_0.3.0

Total time elapsed

## [1] "Elapsed Time: 9.989 mins"

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